28-year-old Saiful Bukhari, who was an aide in Anwar's office, had accused the leader of opposition of sodomising him in 2008. Anwar, 65, had denied the charges.
"What Anwar did to my son was real and it was not a political conspiracy against Anwar," Azlan Mohd Lazim, the father of Saiful, was quoted as saying by Star online.
Azlan, however, refused to explain the reason for his sudden retraction, merely saying that he had "repented" and realised that his family was more important to him.
Azlan also announced his immediate resignation from the opposition People's Justice Party.
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Azlan in March had alleged his son was part of a conspiracy hatched by a special officer in the Prime Minister's Department to destroy Anwar's political career.
Anwar was subsequently charged in court with committing sodomy on Saiful but acquitted at the end of the defence's case.
The prosecution has filed an appeal.
Sodomy is illegal in Muslim-majority Malaysia.